Supplementary files: Proteomics datasets of developing rat brain: synaptic proteome and SUMO2/3-ylome.

Supplementary files related to the data article "Proteomics datasets of developing rat brain: synaptic proteome and SUMO2/3-ylome"
Kieffer F., Pronot M., Gay, A.-S., Debayle D. and Gwizdek C., Data in Brief (2022). DOI: 10.1016/j.dib.2022.108151

This article characterizes the synaptic proteome from rat at 14 postnatal days (PND14), a period that combines intense synaptogenesis, neurotransmission and high levels of SUMO2/3-ylation. It complements the publication: Pronot M, Kieffer F, Gay AS, Debayle D, Forquet R, Poupon G, Schorova L, Martin S, Gwizdek C. "Proteomic Identification of an Endogenous Synaptic SUMOylome in the Developing Rat Brain." Front Mol Neurosci. 2021 Nov 23;14:780535. doi: 10.3389/fnmol.2021.780535. eCollection 2021. DOI: 10.3389/fnmol.2021.780535. The synaptosomal fraction was isolated by differential centrifugation on sucrose percoll gradient and the synaptosomal proteome was analyzed by LC-MS/MS. Four biological replicates were performed. The proteins present at least in 3 of the 4 replicates were selected as synaptic components, leading to a list of 4379 proteins.

Supplementary table S1 provides details for enrichment analyses of the 14PND rat brain synaptic proteome for GO terms using generic (clusterProfiler output fed into Revigo ) or synapse specific (SynGO) tools .

Supplementary table S2 provides details for protein-protein interactions between the proteins identified in the developing rat brain synapses, as predicted by the the Cytoscape platform implemented with StringApp. The proteins identified as candidate SUMO2/3 targets according to Pronot et al. (2021) present a SUMO status equal to 1, the others a SUMO status equal to 0.

Supplementary table S3 provides protein lists filtered for "Master Proteins" with a "High" Combined Protein FDR Confidence.